SBGrid Newsletter: December 2023

Dear Consortium Members and Affiliates,

Our monthly recap comes a little early in December, and a bit abbreviated as we wrap things up before the holiday break. Read on for detailed closure dates, a link to our December webinar recording, a reminder about our January DIALS webinar, two new software titles, eight new members to welcome, and two member publication highlights.

The winter break is upon us, when here at Harvard we will close up shop for a bit. SBGrid offices will be closed beginning Friday, December 22nd through Monday, January 1st. We'll keep an eye out for emergencies, but will otherwise be back with you in the new year. Warm wishes for peace and happy holidays to all. 

Many thanks to Robin Pearce for giving us a primer on DeepFoldRNA in last week's software webinar. If you missed the live presentation, you can find the recording on SBGrid's YouTube channel. We'll restart in January with an update from Graeme Winter, Team Leader at Diamond Light Source, with the latest on DIALS  [Register here].

Jan 9:  DIALS - what’s new - with a focus on treatment of multi-crystal data sets - Graeme Winter

Feb 13: OccuPy  - Björn Forsberg
Mar 12:  Relion-5 - Sjors Scheres

Apr 9: RFdiffusion - Brian Trippe

May 14: Free energy methods in Amber - Darrin York

Jun 11: TomoDRGN - Joseph Davis

July 9:  matchmaps - Dennis Brookner

Webinar registration and details

Our December software push includes two new software titles:  CNIO Relion Tools and RxDock. See Software Changes below for complete details.

Eight new members joined SBGrid in December: Emina Stojkovic of Northeastern Illinois University, Harel Weinstein from Weill Cornell Medicine, Katherine Susa of University of California, San Francisco, Wilson Poon from University of Texas at El Paso, and four new members from ETH Zurich: Manuela Hospenthal, Stefanie Jonas, Kaspar Locher, and Michal Wieczorek. Welcome to our newest members!

Over 100 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:

- Fisk University student Vida Storm Robertson highlighted a publication from SBGrid members Jason McLellan and Andrew Ellington of the University of Texas at Austin that appeared in Communication Biology and shows the immune escape capabilities of the COVID-19 Omicron variants and mechanistic observations about how Omicron evades potent antibodies. [Read more]

- Meharry Medical College student KeAndreya Morrison chose a Nature Communications publication from SBGrid member Ramachandran Murali of Cedars-Sinai Medical Center to highlight, which explores the difference between two variations of a Hyaluronidase, HylA and HylB expressed by Cutibacterium acnes that leads to acne-prone and healthy skin, respectively. [Read more]

If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.

SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.

Please use this SBGrid logo on the acknowledgements slide of your presentations.

We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:

Structural biology applications used in this project were compiled and configured by SBGrid [1].

[1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.

Link to article: https://elifesciences.org/articles/01456.

SBGrid's eLife paper received five new citations since our last reporting, from these SBGrid members: Dmitry Lyumkis of Salk Institute and Navtej Toor from University of California, San Diego in Nature Structural and Molecular Biology: Structural basis of branching during RNA splicing; Ramachandran Murali from Cedars-Sinai Medical Center with collaborators from UCSD in Nature Communications: Functional divergence of a bacterial enzyme promotes healthy or acneic skin; Evris Gavathiotis of Albert Einstein College of Medicine in Nature Communications: Chemical modulation of cytosolic BAX homodimer potentiates BAX activation and apoptosis.

CNIO Relion Tools is new to SBGrid at version 8f5dac5. CNIO Relion Tools is a collection of scripts used during cryoEM data collection and analysis with RELION.

RxDock is also new to the collection at release 2013.1.0. RxDock is a cross-platform fork of rDock, a fast and versatile open-source program for docking ligands to proteins and nucleic acids.

Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.

This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium.

More information about the SBGrid Consortium is available at https://sbgrid.org

Report software bugs: sbgrid.org/bugs